The reason the Enterprise
-B has those added bits on the secondary hull (that the stock Excelsior
doesn't) is so they could be easily 'ripped away' by battle damage without harming the rest of the model. GEN was the first Trek film to use CGI, that I'm aware of, but it was only for a few seconds (when it's firing the deflector dish) - the actual ship was a model. So they needed a place where the Nexus energy ribbon could hit the ship but which wouldn't destroy the whole model.